Variant report

Variant	rs917055
Chromosome Location	chr12:48385576-48385577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr12:48384956-48385888	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48373823..48376376-chr12:48383731..48387007,3	MCF-7	breast:
2	chr12:48384703..48387276-chr12:48389834..48391406,2	K562	blood:
3	chr12:48383628..48385806-chr12:48436712..48438837,2	K562	blood:

Variant related genes	Relation type
COL2A1	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1034762	0.86[ASW][hapmap];0.93[CEU][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10783227	0.86[CEU][hapmap];0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11168337	0.80[CHD][hapmap]
rs1621710	0.92[ASN][1000 genomes]
rs1635526	0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1635528	0.84[AMR][1000 genomes]
rs1635529	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1635534	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635535	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635536	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635537	0.86[ASN][1000 genomes]
rs1635544	0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1635546	0.82[ASN][1000 genomes]
rs1635547	0.82[ASN][1000 genomes]
rs1635550	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes]
rs1793911	0.92[ASN][1000 genomes]
rs1793912	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793913	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793915	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1793917	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793923	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1793924	0.92[ASN][1000 genomes]
rs1793931	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1793933	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1793955	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1793956	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1859444	0.87[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1990029	0.93[CEU][hapmap]
rs3803183	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3803184	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3825404	0.87[CEU][hapmap];0.81[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6580647	0.87[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap]
rs6580649	0.87[CEU][hapmap];0.80[GIH][hapmap]
rs7305954	0.94[GIH][hapmap]
rs740024	0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9805048	0.94[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs917055	ZNF641	cis	Whole Blood	GTEx
rs917055	SNORA2A	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48381200-48385800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:48381400-48386400	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:48381400-48386800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48381400-48388800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:48382800-48385800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
7	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:48383000-48385600	Enhancers	Spleen	Spleen
9	chr12:48383000-48388400	Weak transcription	Psoas Muscle	Psoas
10	chr12:48383200-48385600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:48383200-48385600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:48383200-48385600	Enhancers	Dnd41	blood
13	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:48384000-48386000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr12:48384200-48387600	Enhancers	Fetal Lung	lung
17	chr12:48384400-48386200	Enhancers	Fetal Brain Female	brain
18	chr12:48384400-48386400	Enhancers	Fetal Brain Male	brain
19	chr12:48384400-48386600	Bivalent Enhancer	Fetal Stomach	stomach
20	chr12:48384600-48386000	Enhancers	Placenta	Placenta
21	chr12:48384600-48386400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:48384600-48386400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr12:48384800-48385800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:48384800-48386200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:48384800-48386200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr12:48385000-48385600	Enhancers	Right Atrium	heart
27	chr12:48385000-48385600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr12:48385000-48385800	Enhancers	Lung	lung
29	chr12:48385000-48385800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
30	chr12:48385000-48386000	Enhancers	Right Ventricle	heart
31	chr12:48385200-48385800	Enhancers	Fetal Heart	heart
32	chr12:48385200-48386000	Enhancers	Brain Germinal Matrix	brain
33	chr12:48385200-48391600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:48385400-48385600	Enhancers	Esophagus	oesophagus
35	chr12:48385400-48385800	Enhancers	Left Ventricle	heart
36	chr12:48385400-48386200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:48385400-48386400	Bivalent Enhancer	Fetal Muscle Leg	muscle

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